Reconstructions and analyses of mouse cortex Layer 2/3 serial EM volume
Attribution: https://www.microns-explorer.org/terms-and-conditions
Citation: https://www.microns-explorer.org/citation-policy
For an intriguing summary of this revolution, read Mitch Glickstein’s essay on Golgi and Cajal in Cell.
Pyramidal neuron of the mouse cortex stained using the Golgi method
Image credit: I created this serial LM reconstruction of a Golgi-stained mouse pyramidal neuron using a Zeiss Photomicroscope II at 40x oil and Smart Objects in Photoshop.
Petabytes of data have been generated for small volumes (1 cubic mm or less) of human, mouse, songbird, and fly brain volumes. This gargantuan task has been spearheaded by investigators from a variety of entities, including Allen Institute, Baylor, Columbia, Google Research, Harvard, IARPA, Janelia/HHMI, Johns Hopkins, Max Planck Institute, Princeton, Rice, and the University of Cambridge, among others.
Pyramdial neuron from the Layer 2/3 serial EM volume
Image credit, I created this reconstruction using Neuroglancer of pyramidal neuron with cellid 648518346349538440 in the Layer 2/3 volume.
This github repo focuses on visualization and analyses of the Layer 2/3 EM volume data generated in the IARPA Microns consortium (Allen Institute, Baylor, Princeton). The volume can be viewed in Neuroglancer (developed at Google Research). Allen Institute and the Seung lab at Princeton have posted datasets, resources, analysis tools, and more on their respective github repos, and also at the Allen Brain Map website.
Use lookup_cellid_in_layer23_volume.ipynb to identify
the cell subtype for a given cellid in the Layer 2/3 volume. This is a
human-curated list for cells that contain all (or most) of the cell soma
within the volume.
Use lookup_mitochondria_ids.ipynb to look up
mitochondria ids by cellid. Useful for creating a list of mito ids for
visualization in neuroglancer and for analyzing voxel data.
Use lookup_synapse_ids.ipynb to look up synapse ids by
pre- and post-synaptic cell ids. Also contains voxel data.
Use synapse_visualizer.ipynb to create a 2D and 3D
visualization of all pre- and post-synaptic sites on a cell of
interest.
axon_carrying_dendrite
folder: a partial neuron (soma is not in the volume) with a possible
axon-carrying dendrite.
axon-carrying dendrite
autapses
folder: there are three autapses in the Layer 2/3 volume and many
(24) cases of segmenation errors that are not true autapses.
inhibitory basket neuron autapse
mitochondria
folder: analysis of interesting mitochondrial features in the layer
2/3 volume, including the largest contiguous mitochondrion in an
astrocyte, and the largest number of mitochondria by count in an
inhibitory basket neuron.
large contiguous mitochondria in an astrocyte
most_synapses
folder: reconstructions and synaptic analyses of an excitatory
pyramidal neuron with the most synapses in the volume, along with an
inhibitory basket neuron making the most synapses onto other processes
within the volume.
neuron with the most synpases in the layer 2/3 volume
Pairs of neurons in the Layer 2/3 volume that synapse onto one another
reciprocal_pairs
folder: Martinotti-bipolar reciprocal pair (cell ids
648518346349538179 and 648518346349515986, respectively).
Martinotti-bipolar reciprocal pair
oligodendrocyte_648518346349508279
folder: a beautiful example of an oligocyte in the layer 2/3 volume.
Images of myelination as well as an example of mis-segmentation where a
synaptic bouton from a nearby axon was incorrectly segmented to the
oligodendrocyte cell.
oligodendrocyte myelinating a neuronal process
Drop me an email if you have any questions or would like to collaborate. Shawn